1 Data preparation

1.1 Outline

  • Load scripts: loads libraries and useful scripts used in the analyses; all .R files contained in scripts at the root of the factory are automatically loaded

  • Load data: imports datasets, and may contain some ad hoc changes to the data such as specific data cleaning (not used in other reports), new variables used in the analyses, etc.

1.2 Load packages


library(reportfactory)
library(here)
library(rio) 
library(tidyverse)
library(incidence)
library(distcrete)
library(epitrix)
library(earlyR)
library(projections)
library(linelist)
library(remotes)
library(janitor)
library(kableExtra)
library(DT)
library(cyphr)
library(chngpt)
library(lubridate)
library(ggpubr)
library(ggnewscale)

1.3 Load scripts

These scripts will load:

  • all scripts stored as .R files inside /scripts/
  • all scripts stored as .R files inside /src/

These scripts also contain routines to access the latest clean encrypted data (see next section).


reportfactory::rfh_load_scripts()

1.4 Load clean data

We import the latest NHS pathways data:


x <- import_pathways() %>%
  as_tibble()
x
## # A tibble: 449,644 x 11
##    site_type date       sex    age   ccg_code ccg_name count postcode nhs_region
##    <chr>     <date>     <chr>  <chr> <chr>    <chr>    <int> <chr>    <chr>     
##  1 111       2020-03-18 female miss… e380000… nhs_glo…     1 gl34fe   South West
##  2 111       2020-03-18 female miss… e380001… nhs_sou…     1 ne325nn  North Eas…
##  3 111       2020-03-18 female 0-18  e380000… nhs_air…     8 bd57jr   North Eas…
##  4 111       2020-03-18 female 0-18  e380000… nhs_ash…     7 tn254ab  South East
##  5 111       2020-03-18 female 0-18  e380000… nhs_bar…    35 rm13ae   London    
##  6 111       2020-03-18 female 0-18  e380000… nhs_bar…     9 n111np   London    
##  7 111       2020-03-18 female 0-18  e380000… nhs_bar…    11 s752py   North Eas…
##  8 111       2020-03-18 female 0-18  e380000… nhs_bas…    19 ss143hg  East of E…
##  9 111       2020-03-18 female 0-18  e380000… nhs_bas…     6 dn227xf  North Eas…
## 10 111       2020-03-18 female 0-18  e380000… nhs_bat…     9 ba25rp   South West
## # … with 449,634 more rows, and 2 more variables: day <int>, weekday <fct>

We also import demographics data for NHS regions in England, used later in our analysis:


path <- here::here("data", "csv", "nhs_region_population_2018.csv")
nhs_region_pop <- rio::import(path) %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

nhs_region_pop$nhs_region <- gsub(" Of ", " of ", nhs_region_pop$nhs_region)
nhs_region_pop$nhs_region <- gsub(" And ", " and ", nhs_region_pop$nhs_region)
nhs_region_pop
##                  nhs_region variable      value
## 1                North West     0-18 0.22538599
## 2  North East and Yorkshire     0-18 0.21876449
## 3                  Midlands     0-18 0.22564656
## 4           East of England     0-18 0.22810783
## 5                    London     0-18 0.23764782
## 6                South East     0-18 0.22458811
## 7                South West     0-18 0.20799797
## 8                North West    19-69 0.64274078
## 9  North East and Yorkshire    19-69 0.64437753
## 10                 Midlands    19-69 0.63876675
## 11          East of England    19-69 0.63034229
## 12                   London    19-69 0.67820084
## 13               South East    19-69 0.63267336
## 14               South West    19-69 0.63176131
## 15               North West   70-120 0.13187323
## 16 North East and Yorkshire   70-120 0.13685797
## 17                 Midlands   70-120 0.13558669
## 18          East of England   70-120 0.14154988
## 19                   London   70-120 0.08415135
## 20               South East   70-120 0.14273853
## 21               South West   70-120 0.16024072

Finally, we import publically available deaths per NHS region:


dth <- import_deaths() %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

#truncation to account for reporting delay
delay_max <- 21

dth$nhs_region <- gsub(" Of ", " of ", dth$nhs_region)
dth$nhs_region <- gsub(" And ", " and ", dth$nhs_region)
dth
##      date_report               nhs_region deaths
## 1     2020-03-01          East of England      0
## 2     2020-03-02          East of England      1
## 3     2020-03-03          East of England      0
## 4     2020-03-04          East of England      0
## 5     2020-03-05          East of England      0
## 6     2020-03-06          East of England      1
## 7     2020-03-07          East of England      0
## 8     2020-03-08          East of England      0
## 9     2020-03-09          East of England      1
## 10    2020-03-10          East of England      0
## 11    2020-03-11          East of England      0
## 12    2020-03-12          East of England      0
## 13    2020-03-13          East of England      1
## 14    2020-03-14          East of England      2
## 15    2020-03-15          East of England      2
## 16    2020-03-16          East of England      1
## 17    2020-03-17          East of England      1
## 18    2020-03-18          East of England      5
## 19    2020-03-19          East of England      4
## 20    2020-03-20          East of England      2
## 21    2020-03-21          East of England     11
## 22    2020-03-22          East of England     12
## 23    2020-03-23          East of England     11
## 24    2020-03-24          East of England     19
## 25    2020-03-25          East of England     26
## 26    2020-03-26          East of England     36
## 27    2020-03-27          East of England     38
## 28    2020-03-28          East of England     28
## 29    2020-03-29          East of England     43
## 30    2020-03-30          East of England     45
## 31    2020-03-31          East of England     70
## 32    2020-04-01          East of England     63
## 33    2020-04-02          East of England     65
## 34    2020-04-03          East of England     80
## 35    2020-04-04          East of England     71
## 36    2020-04-05          East of England     76
## 37    2020-04-06          East of England     71
## 38    2020-04-07          East of England     93
## 39    2020-04-08          East of England    111
## 40    2020-04-09          East of England     87
## 41    2020-04-10          East of England     74
## 42    2020-04-11          East of England     92
## 43    2020-04-12          East of England    100
## 44    2020-04-13          East of England     78
## 45    2020-04-14          East of England     61
## 46    2020-04-15          East of England     82
## 47    2020-04-16          East of England     74
## 48    2020-04-17          East of England     86
## 49    2020-04-18          East of England     64
## 50    2020-04-19          East of England     67
## 51    2020-04-20          East of England     67
## 52    2020-04-21          East of England     75
## 53    2020-04-22          East of England     67
## 54    2020-04-23          East of England     49
## 55    2020-04-24          East of England     66
## 56    2020-04-25          East of England     54
## 57    2020-04-26          East of England     48
## 58    2020-04-27          East of England     46
## 59    2020-04-28          East of England     58
## 60    2020-04-29          East of England     32
## 61    2020-04-30          East of England     45
## 62    2020-05-01          East of England     49
## 63    2020-05-02          East of England     29
## 64    2020-05-03          East of England     41
## 65    2020-05-04          East of England     19
## 66    2020-05-05          East of England     36
## 67    2020-05-06          East of England     31
## 68    2020-05-07          East of England     33
## 69    2020-05-08          East of England     33
## 70    2020-05-09          East of England     29
## 71    2020-05-10          East of England     22
## 72    2020-05-11          East of England     18
## 73    2020-05-12          East of England     21
## 74    2020-05-13          East of England     27
## 75    2020-05-14          East of England     26
## 76    2020-05-15          East of England     19
## 77    2020-05-16          East of England     26
## 78    2020-05-17          East of England     17
## 79    2020-05-18          East of England     25
## 80    2020-05-19          East of England     15
## 81    2020-05-20          East of England     26
## 82    2020-05-21          East of England     21
## 83    2020-05-22          East of England     13
## 84    2020-05-23          East of England     12
## 85    2020-05-24          East of England     17
## 86    2020-05-25          East of England     25
## 87    2020-05-26          East of England     14
## 88    2020-05-27          East of England     12
## 89    2020-05-28          East of England     17
## 90    2020-05-29          East of England     16
## 91    2020-05-30          East of England      9
## 92    2020-05-31          East of England      8
## 93    2020-06-01          East of England     17
## 94    2020-06-02          East of England     14
## 95    2020-06-03          East of England     10
## 96    2020-06-04          East of England      7
## 97    2020-06-05          East of England     14
## 98    2020-06-06          East of England      5
## 99    2020-06-07          East of England      9
## 100   2020-06-08          East of England      7
## 101   2020-06-09          East of England      6
## 102   2020-06-10          East of England      8
## 103   2020-06-11          East of England      1
## 104   2020-06-12          East of England      9
## 105   2020-06-13          East of England      5
## 106   2020-06-14          East of England      4
## 107   2020-06-15          East of England      8
## 108   2020-06-16          East of England      3
## 109   2020-06-17          East of England      7
## 110   2020-06-18          East of England      4
## 111   2020-06-19          East of England      7
## 112   2020-06-20          East of England      4
## 113   2020-06-21          East of England      3
## 114   2020-06-22          East of England      6
## 115   2020-06-23          East of England      5
## 116   2020-06-24          East of England      4
## 117   2020-06-25          East of England      1
## 118   2020-06-26          East of England      5
## 119   2020-06-27          East of England      6
## 120   2020-06-28          East of England      8
## 121   2020-06-29          East of England      4
## 122   2020-06-30          East of England      5
## 123   2020-07-01          East of England      2
## 124   2020-07-02          East of England      5
## 125   2020-07-03          East of England      0
## 126   2020-07-04          East of England      3
## 127   2020-07-05          East of England      1
## 128   2020-07-06          East of England      2
## 129   2020-07-07          East of England      2
## 130   2020-07-08          East of England      0
## 131   2020-07-09          East of England      8
## 132   2020-07-10          East of England      4
## 133   2020-07-11          East of England      2
## 134   2020-07-12          East of England      1
## 135   2020-07-13          East of England      8
## 136   2020-07-14          East of England      2
## 137   2020-07-15          East of England      0
## 138   2020-07-16          East of England      0
## 139   2020-07-17          East of England      0
## 140   2020-07-18          East of England      0
## 141   2020-07-19          East of England      1
## 142   2020-07-20          East of England      1
## 143   2020-07-21          East of England      1
## 144   2020-07-22          East of England      2
## 145   2020-07-23          East of England      1
## 146   2020-07-24          East of England      1
## 147   2020-07-25          East of England      0
## 148   2020-07-26          East of England      1
## 149   2020-07-27          East of England      1
## 150   2020-07-28          East of England      2
## 151   2020-07-29          East of England      0
## 152   2020-07-30          East of England      0
## 153   2020-07-31          East of England      1
## 154   2020-08-01          East of England      0
## 155   2020-08-02          East of England      0
## 156   2020-08-03          East of England      0
## 157   2020-08-04          East of England      1
## 158   2020-08-05          East of England      1
## 159   2020-08-06          East of England      0
## 160   2020-08-07          East of England      1
## 161   2020-08-08          East of England      0
## 162   2020-08-09          East of England      0
## 163   2020-08-10          East of England      1
## 164   2020-08-11          East of England      2
## 165   2020-08-12          East of England      1
## 166   2020-08-13          East of England      0
## 167   2020-08-14          East of England      1
## 168   2020-08-15          East of England      1
## 169   2020-08-16          East of England      0
## 170   2020-08-17          East of England      0
## 171   2020-08-18          East of England      2
## 172   2020-08-19          East of England      1
## 173   2020-08-20          East of England      1
## 174   2020-08-21          East of England      0
## 175   2020-08-22          East of England      1
## 176   2020-08-23          East of England      1
## 177   2020-08-24          East of England      0
## 178   2020-08-25          East of England      0
## 179   2020-08-26          East of England      1
## 180   2020-08-27          East of England      1
## 181   2020-08-28          East of England      0
## 182   2020-08-29          East of England      0
## 183   2020-08-30          East of England      0
## 184   2020-08-31          East of England      0
## 185   2020-09-01          East of England      0
## 186   2020-09-02          East of England      0
## 187   2020-09-03          East of England      1
## 188   2020-09-04          East of England      1
## 189   2020-09-05          East of England      0
## 190   2020-09-06          East of England      1
## 191   2020-09-07          East of England      0
## 192   2020-09-08          East of England      0
## 193   2020-09-09          East of England      0
## 194   2020-09-10          East of England      0
## 195   2020-09-11          East of England      0
## 196   2020-09-12          East of England      0
## 197   2020-09-13          East of England      1
## 198   2020-09-14          East of England      1
## 199   2020-09-15          East of England      0
## 200   2020-09-16          East of England      0
## 201   2020-09-17          East of England      0
## 202   2020-09-18          East of England      0
## 203   2020-09-19          East of England      0
## 204   2020-09-20          East of England      2
## 205   2020-09-21          East of England      0
## 206   2020-09-22          East of England      2
## 207   2020-09-23          East of England      1
## 208   2020-09-24          East of England      0
## 209   2020-09-25          East of England      1
## 210   2020-09-26          East of England      1
## 211   2020-09-27          East of England      1
## 212   2020-09-28          East of England      2
## 213   2020-09-29          East of England      2
## 214   2020-09-30          East of England      2
## 215   2020-10-01          East of England      2
## 216   2020-10-02          East of England      1
## 217   2020-10-03          East of England      1
## 218   2020-10-04          East of England      0
## 219   2020-10-05          East of England      0
## 220   2020-10-06          East of England      4
## 221   2020-10-07          East of England      6
## 222   2020-10-08          East of England      3
## 223   2020-10-09          East of England      1
## 224   2020-10-10          East of England      6
## 225   2020-10-11          East of England      2
## 226   2020-10-12          East of England      2
## 227   2020-10-13          East of England      1
## 228   2020-10-14          East of England      3
## 229   2020-10-15          East of England      4
## 230   2020-10-16          East of England      5
## 231   2020-10-17          East of England      6
## 232   2020-10-18          East of England      7
## 233   2020-10-19          East of England      5
## 234   2020-10-20          East of England      9
## 235   2020-10-21          East of England      8
## 236   2020-10-22          East of England      7
## 237   2020-10-23          East of England     14
## 238   2020-10-24          East of England      1
## 239   2020-10-25          East of England     10
## 240   2020-10-26          East of England     10
## 241   2020-10-27          East of England      8
## 242   2020-10-28          East of England     12
## 243   2020-10-29          East of England     10
## 244   2020-10-30          East of England     12
## 245   2020-10-31          East of England     15
## 246   2020-11-01          East of England     14
## 247   2020-11-02          East of England      9
## 248   2020-11-03          East of England     14
## 249   2020-11-04          East of England     11
## 250   2020-11-05          East of England     12
## 251   2020-11-06          East of England     18
## 252   2020-11-07          East of England     10
## 253   2020-11-08          East of England     13
## 254   2020-11-09          East of England     16
## 255   2020-11-10          East of England     26
## 256   2020-11-11          East of England     14
## 257   2020-11-12          East of England     14
## 258   2020-11-13          East of England     21
## 259   2020-11-14          East of England     19
## 260   2020-11-15          East of England     13
## 261   2020-11-16          East of England     11
## 262   2020-11-17          East of England     17
## 263   2020-11-18          East of England     19
## 264   2020-11-19          East of England     23
## 265   2020-11-20          East of England     24
## 266   2020-11-21          East of England     19
## 267   2020-11-22          East of England     21
## 268   2020-11-23          East of England     18
## 269   2020-11-24          East of England     21
## 270   2020-11-25          East of England     19
## 271   2020-11-26          East of England     19
## 272   2020-11-27          East of England     14
## 273   2020-11-28          East of England     28
## 274   2020-11-29          East of England     19
## 275   2020-11-30          East of England     22
## 276   2020-12-01          East of England     26
## 277   2020-12-02          East of England     18
## 278   2020-12-03          East of England     24
## 279   2020-12-04          East of England     25
## 280   2020-12-05          East of England     25
## 281   2020-12-06          East of England     21
## 282   2020-12-07          East of England     16
## 283   2020-12-08          East of England     26
## 284   2020-12-09          East of England     19
## 285   2020-12-10          East of England     32
## 286   2020-12-11          East of England     32
## 287   2020-12-12          East of England     27
## 288   2020-12-13          East of England     25
## 289   2020-12-14          East of England     32
## 290   2020-12-15          East of England     35
## 291   2020-12-16          East of England     29
## 292   2020-12-17          East of England     42
## 293   2020-12-18          East of England     44
## 294   2020-12-19          East of England     54
## 295   2020-12-20          East of England     52
## 296   2020-12-21          East of England     66
## 297   2020-12-22          East of England     52
## 298   2020-12-23          East of England     62
## 299   2020-12-24          East of England     61
## 300   2020-12-25          East of England     58
## 301   2020-12-26          East of England     64
## 302   2020-12-27          East of England     54
## 303   2020-12-28          East of England     71
## 304   2020-12-29          East of England     54
## 305   2020-12-30          East of England     76
## 306   2020-12-31          East of England     82
## 307   2021-01-01          East of England     89
## 308   2021-01-02          East of England     66
## 309   2021-01-03          East of England     78
## 310   2021-01-04          East of England     87
## 311   2021-01-05          East of England    102
## 312   2021-01-06          East of England    100
## 313   2021-01-07          East of England    116
## 314   2021-01-08          East of England     95
## 315   2021-01-09          East of England    133
## 316   2021-01-10          East of England    124
## 317   2021-01-11          East of England    126
## 318   2021-01-12          East of England    131
## 319   2021-01-13          East of England    131
## 320   2021-01-14          East of England    126
## 321   2021-01-15          East of England    118
## 322   2021-01-16          East of England    130
## 323   2021-01-17          East of England    132
## 324   2021-01-18          East of England    120
## 325   2021-01-19          East of England    128
## 326   2021-01-20          East of England    147
## 327   2021-01-21          East of England    133
## 328   2021-01-22          East of England    122
## 329   2021-01-23          East of England    102
## 330   2021-01-24          East of England    101
## 331   2021-01-25          East of England    111
## 332   2021-01-26          East of England     87
## 333   2021-01-27          East of England     94
## 334   2021-01-28          East of England    110
## 335   2021-01-29          East of England     95
## 336   2021-01-30          East of England     84
## 337   2021-01-31          East of England     71
## 338   2021-02-01          East of England     63
## 339   2021-02-02          East of England     73
## 340   2021-02-03          East of England     80
## 341   2021-02-04          East of England     75
## 342   2021-02-05          East of England     65
## 343   2021-02-06          East of England     76
## 344   2021-02-07          East of England     61
## 345   2021-02-08          East of England     73
## 346   2021-02-09          East of England     62
## 347   2021-02-10          East of England     49
## 348   2021-02-11          East of England     52
## 349   2021-02-12          East of England     47
## 350   2021-02-13          East of England     45
## 351   2021-02-14          East of England     31
## 352   2021-02-15          East of England     47
## 353   2021-02-16          East of England     45
## 354   2021-02-17          East of England     46
## 355   2021-02-18          East of England     29
## 356   2021-02-19          East of England     27
## 357   2021-02-20          East of England     29
## 358   2021-02-21          East of England     23
## 359   2021-02-22          East of England     25
## 360   2021-02-23          East of England     23
## 361   2021-02-24          East of England     12
## 362   2021-02-25          East of England      1
## 363   2020-03-01                   London      0
## 364   2020-03-02                   London      0
## 365   2020-03-03                   London      0
## 366   2020-03-04                   London      0
## 367   2020-03-05                   London      0
## 368   2020-03-06                   London      1
## 369   2020-03-07                   London      0
## 370   2020-03-08                   London      0
## 371   2020-03-09                   London      1
## 372   2020-03-10                   London      0
## 373   2020-03-11                   London      5
## 374   2020-03-12                   London      6
## 375   2020-03-13                   London     10
## 376   2020-03-14                   London     13
## 377   2020-03-15                   London      9
## 378   2020-03-16                   London     15
## 379   2020-03-17                   London     23
## 380   2020-03-18                   London     28
## 381   2020-03-19                   London     25
## 382   2020-03-20                   London     44
## 383   2020-03-21                   London     49
## 384   2020-03-22                   London     54
## 385   2020-03-23                   London     63
## 386   2020-03-24                   London     86
## 387   2020-03-25                   London    112
## 388   2020-03-26                   London    130
## 389   2020-03-27                   London    130
## 390   2020-03-28                   London    123
## 391   2020-03-29                   London    145
## 392   2020-03-30                   London    151
## 393   2020-03-31                   London    183
## 394   2020-04-01                   London    202
## 395   2020-04-02                   London    191
## 396   2020-04-03                   London    199
## 397   2020-04-04                   London    231
## 398   2020-04-05                   London    195
## 399   2020-04-06                   London    198
## 400   2020-04-07                   London    220
## 401   2020-04-08                   London    239
## 402   2020-04-09                   London    207
## 403   2020-04-10                   London    171
## 404   2020-04-11                   London    178
## 405   2020-04-12                   London    159
## 406   2020-04-13                   London    166
## 407   2020-04-14                   London    143
## 408   2020-04-15                   London    143
## 409   2020-04-16                   London    140
## 410   2020-04-17                   London    101
## 411   2020-04-18                   London    101
## 412   2020-04-19                   London    104
## 413   2020-04-20                   London     96
## 414   2020-04-21                   London     96
## 415   2020-04-22                   London    109
## 416   2020-04-23                   London     77
## 417   2020-04-24                   London     71
## 418   2020-04-25                   London     58
## 419   2020-04-26                   London     53
## 420   2020-04-27                   London     52
## 421   2020-04-28                   London     44
## 422   2020-04-29                   London     45
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## 1444  2021-02-21 North East and Yorkshire     38
## 1445  2021-02-22 North East and Yorkshire     20
## 1446  2021-02-23 North East and Yorkshire     34
## 1447  2021-02-24 North East and Yorkshire     19
## 1448  2021-02-25 North East and Yorkshire      6
## 1449  2020-03-01               North West      0
## 1450  2020-03-02               North West      0
## 1451  2020-03-03               North West      0
## 1452  2020-03-04               North West      0
## 1453  2020-03-05               North West      1
## 1454  2020-03-06               North West      0
## 1455  2020-03-07               North West      0
## 1456  2020-03-08               North West      1
## 1457  2020-03-09               North West      0
## 1458  2020-03-10               North West      0
## 1459  2020-03-11               North West      0
## 1460  2020-03-12               North West      2
## 1461  2020-03-13               North West      3
## 1462  2020-03-14               North West      1
## 1463  2020-03-15               North West      4
## 1464  2020-03-16               North West      2
## 1465  2020-03-17               North West      4
## 1466  2020-03-18               North West      6
## 1467  2020-03-19               North West      7
## 1468  2020-03-20               North West     10
## 1469  2020-03-21               North West     11
## 1470  2020-03-22               North West     13
## 1471  2020-03-23               North West     15
## 1472  2020-03-24               North West     21
## 1473  2020-03-25               North West     21
## 1474  2020-03-26               North West     29
## 1475  2020-03-27               North West     36
## 1476  2020-03-28               North West     28
## 1477  2020-03-29               North West     46
## 1478  2020-03-30               North West     67
## 1479  2020-03-31               North West     52
## 1480  2020-04-01               North West     86
## 1481  2020-04-02               North West     96
## 1482  2020-04-03               North West     95
## 1483  2020-04-04               North West     98
## 1484  2020-04-05               North West    102
## 1485  2020-04-06               North West    100
## 1486  2020-04-07               North West    136
## 1487  2020-04-08               North West    127
## 1488  2020-04-09               North West    119
## 1489  2020-04-10               North West    117
## 1490  2020-04-11               North West    138
## 1491  2020-04-12               North West    125
## 1492  2020-04-13               North West    130
## 1493  2020-04-14               North West    130
## 1494  2020-04-15               North West    114
## 1495  2020-04-16               North West    135
## 1496  2020-04-17               North West     98
## 1497  2020-04-18               North West    114
## 1498  2020-04-19               North West     71
## 1499  2020-04-20               North West     83
## 1500  2020-04-21               North West     76
## 1501  2020-04-22               North West     87
## 1502  2020-04-23               North West     85
## 1503  2020-04-24               North West     67
## 1504  2020-04-25               North West     67
## 1505  2020-04-26               North West     55
## 1506  2020-04-27               North West     54
## 1507  2020-04-28               North West     57
## 1508  2020-04-29               North West     64
## 1509  2020-04-30               North West     60
## 1510  2020-05-01               North West     45
## 1511  2020-05-02               North West     56
## 1512  2020-05-03               North West     55
## 1513  2020-05-04               North West     48
## 1514  2020-05-05               North West     49
## 1515  2020-05-06               North West     44
## 1516  2020-05-07               North West     50
## 1517  2020-05-08               North West     43
## 1518  2020-05-09               North West     31
## 1519  2020-05-10               North West     42
## 1520  2020-05-11               North West     35
## 1521  2020-05-12               North West     38
## 1522  2020-05-13               North West     25
## 1523  2020-05-14               North West     26
## 1524  2020-05-15               North West     33
## 1525  2020-05-16               North West     32
## 1526  2020-05-17               North West     24
## 1527  2020-05-18               North West     31
## 1528  2020-05-19               North West     35
## 1529  2020-05-20               North West     27
## 1530  2020-05-21               North West     28
## 1531  2020-05-22               North West     26
## 1532  2020-05-23               North West     31
## 1533  2020-05-24               North West     26
## 1534  2020-05-25               North West     31
## 1535  2020-05-26               North West     27
## 1536  2020-05-27               North West     27
## 1537  2020-05-28               North West     28
## 1538  2020-05-29               North West     20
## 1539  2020-05-30               North West     19
## 1540  2020-05-31               North West     13
## 1541  2020-06-01               North West     12
## 1542  2020-06-02               North West     27
## 1543  2020-06-03               North West     22
## 1544  2020-06-04               North West     22
## 1545  2020-06-05               North West     16
## 1546  2020-06-06               North West     26
## 1547  2020-06-07               North West     20
## 1548  2020-06-08               North West     23
## 1549  2020-06-09               North West     17
## 1550  2020-06-10               North West     16
## 1551  2020-06-11               North West     16
## 1552  2020-06-12               North West     11
## 1553  2020-06-13               North West     10
## 1554  2020-06-14               North West     15
## 1555  2020-06-15               North West     16
## 1556  2020-06-16               North West     16
## 1557  2020-06-17               North West     13
## 1558  2020-06-18               North West     14
## 1559  2020-06-19               North West      7
## 1560  2020-06-20               North West     11
## 1561  2020-06-21               North West      8
## 1562  2020-06-22               North West     11
## 1563  2020-06-23               North West     13
## 1564  2020-06-24               North West     13
## 1565  2020-06-25               North West     15
## 1566  2020-06-26               North West      6
## 1567  2020-06-27               North West      7
## 1568  2020-06-28               North West      9
## 1569  2020-06-29               North West      9
## 1570  2020-06-30               North West      7
## 1571  2020-07-01               North West      3
## 1572  2020-07-02               North West      6
## 1573  2020-07-03               North West      7
## 1574  2020-07-04               North West      4
## 1575  2020-07-05               North West      6
## 1576  2020-07-06               North West      9
## 1577  2020-07-07               North West      8
## 1578  2020-07-08               North West      5
## 1579  2020-07-09               North West     10
## 1580  2020-07-10               North West      2
## 1581  2020-07-11               North West      5
## 1582  2020-07-12               North West      0
## 1583  2020-07-13               North West      6
## 1584  2020-07-14               North West      4
## 1585  2020-07-15               North West      5
## 1586  2020-07-16               North West      2
## 1587  2020-07-17               North West      4
## 1588  2020-07-18               North West      5
## 1589  2020-07-19               North West      3
## 1590  2020-07-20               North West      0
## 1591  2020-07-21               North West      2
## 1592  2020-07-22               North West      3
## 1593  2020-07-23               North West      3
## 1594  2020-07-24               North West      1
## 1595  2020-07-25               North West      1
## 1596  2020-07-26               North West      3
## 1597  2020-07-27               North West      1
## 1598  2020-07-28               North West      1
## 1599  2020-07-29               North West      2
## 1600  2020-07-30               North West      2
## 1601  2020-07-31               North West      0
## 1602  2020-08-01               North West      2
## 1603  2020-08-02               North West      1
## 1604  2020-08-03               North West      8
## 1605  2020-08-04               North West      3
## 1606  2020-08-05               North West      2
## 1607  2020-08-06               North West      2
## 1608  2020-08-07               North West      2
## 1609  2020-08-08               North West      2
## 1610  2020-08-09               North West      3
## 1611  2020-08-10               North West      2
## 1612  2020-08-11               North West      3
## 1613  2020-08-12               North West      0
## 1614  2020-08-13               North West      2
## 1615  2020-08-14               North West      2
## 1616  2020-08-15               North West      6
## 1617  2020-08-16               North West      2
## 1618  2020-08-17               North West      1
## 1619  2020-08-18               North West      2
## 1620  2020-08-19               North West      1
## 1621  2020-08-20               North West      1
## 1622  2020-08-21               North West      4
## 1623  2020-08-22               North West      3
## 1624  2020-08-23               North West      5
## 1625  2020-08-24               North West      4
## 1626  2020-08-25               North West      3
## 1627  2020-08-26               North West      4
## 1628  2020-08-27               North West      1
## 1629  2020-08-28               North West      2
## 1630  2020-08-29               North West      0
## 1631  2020-08-30               North West      2
## 1632  2020-08-31               North West      3
## 1633  2020-09-01               North West      0
## 1634  2020-09-02               North West      2
## 1635  2020-09-03               North West      1
## 1636  2020-09-04               North West      3
## 1637  2020-09-05               North West      6
## 1638  2020-09-06               North West      1
## 1639  2020-09-07               North West      8
## 1640  2020-09-08               North West      6
## 1641  2020-09-09               North West      5
## 1642  2020-09-10               North West      5
## 1643  2020-09-11               North West      1
## 1644  2020-09-12               North West      4
## 1645  2020-09-13               North West      2
## 1646  2020-09-14               North West      4
## 1647  2020-09-15               North West      4
## 1648  2020-09-16               North West      6
## 1649  2020-09-17               North West      7
## 1650  2020-09-18               North West      6
## 1651  2020-09-19               North West      3
## 1652  2020-09-20               North West      2
## 1653  2020-09-21               North West      2
## 1654  2020-09-22               North West      9
## 1655  2020-09-23               North West     14
## 1656  2020-09-24               North West     10
## 1657  2020-09-25               North West      8
## 1658  2020-09-26               North West     14
## 1659  2020-09-27               North West     11
## 1660  2020-09-28               North West     15
## 1661  2020-09-29               North West     12
## 1662  2020-09-30               North West     17
## 1663  2020-10-01               North West     17
## 1664  2020-10-02               North West     20
## 1665  2020-10-03               North West     15
## 1666  2020-10-04               North West     15
## 1667  2020-10-05               North West     15
## 1668  2020-10-06               North West     20
## 1669  2020-10-07               North West     20
## 1670  2020-10-08               North West     22
## 1671  2020-10-09               North West     24
## 1672  2020-10-10               North West     31
## 1673  2020-10-11               North West     31
## 1674  2020-10-12               North West     35
## 1675  2020-10-13               North West     26
## 1676  2020-10-14               North West     35
## 1677  2020-10-15               North West     36
## 1678  2020-10-16               North West     34
## 1679  2020-10-17               North West     52
## 1680  2020-10-18               North West     40
## 1681  2020-10-19               North West     43
## 1682  2020-10-20               North West     48
## 1683  2020-10-21               North West     51
## 1684  2020-10-22               North West     49
## 1685  2020-10-23               North West     50
## 1686  2020-10-24               North West     51
## 1687  2020-10-25               North West     63
## 1688  2020-10-26               North West     53
## 1689  2020-10-27               North West     49
## 1690  2020-10-28               North West     57
## 1691  2020-10-29               North West     74
## 1692  2020-10-30               North West     73
## 1693  2020-10-31               North West     63
## 1694  2020-11-01               North West     76
## 1695  2020-11-02               North West     65
## 1696  2020-11-03               North West     77
## 1697  2020-11-04               North West     64
## 1698  2020-11-05               North West     67
## 1699  2020-11-06               North West     76
## 1700  2020-11-07               North West     79
## 1701  2020-11-08               North West     83
## 1702  2020-11-09               North West     82
## 1703  2020-11-10               North West     68
## 1704  2020-11-11               North West     62
## 1705  2020-11-12               North West     64
## 1706  2020-11-13               North West     81
## 1707  2020-11-14               North West     61
## 1708  2020-11-15               North West     75
## 1709  2020-11-16               North West     74
## 1710  2020-11-17               North West     73
## 1711  2020-11-18               North West     71
## 1712  2020-11-19               North West     67
## 1713  2020-11-20               North West     52
## 1714  2020-11-21               North West     68
## 1715  2020-11-22               North West     52
## 1716  2020-11-23               North West     54
## 1717  2020-11-24               North West     64
## 1718  2020-11-25               North West     65
## 1719  2020-11-26               North West     53
## 1720  2020-11-27               North West     51
## 1721  2020-11-28               North West     46
## 1722  2020-11-29               North West     54
## 1723  2020-11-30               North West     48
## 1724  2020-12-01               North West     53
## 1725  2020-12-02               North West     48
## 1726  2020-12-03               North West     46
## 1727  2020-12-04               North West     48
## 1728  2020-12-05               North West     37
## 1729  2020-12-06               North West     43
## 1730  2020-12-07               North West     50
## 1731  2020-12-08               North West     49
## 1732  2020-12-09               North West     48
## 1733  2020-12-10               North West     49
## 1734  2020-12-11               North West     41
## 1735  2020-12-12               North West     48
## 1736  2020-12-13               North West     41
## 1737  2020-12-14               North West     51
## 1738  2020-12-15               North West     34
## 1739  2020-12-16               North West     41
## 1740  2020-12-17               North West     26
## 1741  2020-12-18               North West     47
## 1742  2020-12-19               North West     45
## 1743  2020-12-20               North West     37
## 1744  2020-12-21               North West     51
## 1745  2020-12-22               North West     52
## 1746  2020-12-23               North West     50
## 1747  2020-12-24               North West     58
## 1748  2020-12-25               North West     52
## 1749  2020-12-26               North West     56
## 1750  2020-12-27               North West     50
## 1751  2020-12-28               North West     48
## 1752  2020-12-29               North West     49
## 1753  2020-12-30               North West     49
## 1754  2020-12-31               North West     62
## 1755  2021-01-01               North West     54
## 1756  2021-01-02               North West     55
## 1757  2021-01-03               North West     57
## 1758  2021-01-04               North West     51
## 1759  2021-01-05               North West     56
## 1760  2021-01-06               North West     69
## 1761  2021-01-07               North West     61
## 1762  2021-01-08               North West     63
## 1763  2021-01-09               North West     65
## 1764  2021-01-10               North West     65
## 1765  2021-01-11               North West     79
## 1766  2021-01-12               North West     65
## 1767  2021-01-13               North West     85
## 1768  2021-01-14               North West     91
## 1769  2021-01-15               North West     84
## 1770  2021-01-16               North West     81
## 1771  2021-01-17               North West     79
## 1772  2021-01-18               North West     92
## 1773  2021-01-19               North West     92
## 1774  2021-01-20               North West     87
## 1775  2021-01-21               North West     85
## 1776  2021-01-22               North West    109
## 1777  2021-01-23               North West    103
## 1778  2021-01-24               North West     95
## 1779  2021-01-25               North West     85
## 1780  2021-01-26               North West    101
## 1781  2021-01-27               North West    104
## 1782  2021-01-28               North West    102
## 1783  2021-01-29               North West     97
## 1784  2021-01-30               North West     76
## 1785  2021-01-31               North West     83
## 1786  2021-02-01               North West     96
## 1787  2021-02-02               North West     82
## 1788  2021-02-03               North West     71
## 1789  2021-02-04               North West     79
## 1790  2021-02-05               North West     67
## 1791  2021-02-06               North West     62
## 1792  2021-02-07               North West     53
## 1793  2021-02-08               North West     73
## 1794  2021-02-09               North West     68
## 1795  2021-02-10               North West     71
## 1796  2021-02-11               North West     66
## 1797  2021-02-12               North West     67
## 1798  2021-02-13               North West     60
## 1799  2021-02-14               North West     50
## 1800  2021-02-15               North West     54
## 1801  2021-02-16               North West     51
## 1802  2021-02-17               North West     55
## 1803  2021-02-18               North West     50
## 1804  2021-02-19               North West     38
## 1805  2021-02-20               North West     29
## 1806  2021-02-21               North West     34
## 1807  2021-02-22               North West     24
## 1808  2021-02-23               North West     28
## 1809  2021-02-24               North West     24
## 1810  2021-02-25               North West      5
## 1811  2020-03-01               South East      0
## 1812  2020-03-02               South East      0
## 1813  2020-03-03               South East      1
## 1814  2020-03-04               South East      0
## 1815  2020-03-05               South East      1
## 1816  2020-03-06               South East      0
## 1817  2020-03-07               South East      0
## 1818  2020-03-08               South East      1
## 1819  2020-03-09               South East      1
## 1820  2020-03-10               South East      1
## 1821  2020-03-11               South East      1
## 1822  2020-03-12               South East      0
## 1823  2020-03-13               South East      1
## 1824  2020-03-14               South East      1
## 1825  2020-03-15               South East      5
## 1826  2020-03-16               South East      8
## 1827  2020-03-17               South East      7
## 1828  2020-03-18               South East     10
## 1829  2020-03-19               South East      9
## 1830  2020-03-20               South East     13
## 1831  2020-03-21               South East      7
## 1832  2020-03-22               South East     25
## 1833  2020-03-23               South East     20
## 1834  2020-03-24               South East     22
## 1835  2020-03-25               South East     29
## 1836  2020-03-26               South East     35
## 1837  2020-03-27               South East     36
## 1838  2020-03-28               South East     36
## 1839  2020-03-29               South East     55
## 1840  2020-03-30               South East     58
## 1841  2020-03-31               South East     65
## 1842  2020-04-01               South East     66
## 1843  2020-04-02               South East     55
## 1844  2020-04-03               South East     72
## 1845  2020-04-04               South East     80
## 1846  2020-04-05               South East     82
## 1847  2020-04-06               South East     88
## 1848  2020-04-07               South East    100
## 1849  2020-04-08               South East     83
## 1850  2020-04-09               South East    104
## 1851  2020-04-10               South East     88
## 1852  2020-04-11               South East     88
## 1853  2020-04-12               South East     88
## 1854  2020-04-13               South East     84
## 1855  2020-04-14               South East     65
## 1856  2020-04-15               South East     72
## 1857  2020-04-16               South East     56
## 1858  2020-04-17               South East     86
## 1859  2020-04-18               South East     57
## 1860  2020-04-19               South East     70
## 1861  2020-04-20               South East     87
## 1862  2020-04-21               South East     51
## 1863  2020-04-22               South East     54
## 1864  2020-04-23               South East     57
## 1865  2020-04-24               South East     64
## 1866  2020-04-25               South East     51
## 1867  2020-04-26               South East     51
## 1868  2020-04-27               South East     41
## 1869  2020-04-28               South East     40
## 1870  2020-04-29               South East     47
## 1871  2020-04-30               South East     29
## 1872  2020-05-01               South East     37
## 1873  2020-05-02               South East     36
## 1874  2020-05-03               South East     17
## 1875  2020-05-04               South East     35
## 1876  2020-05-05               South East     29
## 1877  2020-05-06               South East     25
## 1878  2020-05-07               South East     27
## 1879  2020-05-08               South East     26
## 1880  2020-05-09               South East     28
## 1881  2020-05-10               South East     19
## 1882  2020-05-11               South East     25
## 1883  2020-05-12               South East     27
## 1884  2020-05-13               South East     18
## 1885  2020-05-14               South East     32
## 1886  2020-05-15               South East     25
## 1887  2020-05-16               South East     22
## 1888  2020-05-17               South East     18
## 1889  2020-05-18               South East     23
## 1890  2020-05-19               South East     12
## 1891  2020-05-20               South East     22
## 1892  2020-05-21               South East     15
## 1893  2020-05-22               South East     17
## 1894  2020-05-23               South East     21
## 1895  2020-05-24               South East     17
## 1896  2020-05-25               South East     13
## 1897  2020-05-26               South East     19
## 1898  2020-05-27               South East     19
## 1899  2020-05-28               South East     12
## 1900  2020-05-29               South East     22
## 1901  2020-05-30               South East      8
## 1902  2020-05-31               South East     12
## 1903  2020-06-01               South East     11
## 1904  2020-06-02               South East     13
## 1905  2020-06-03               South East     18
## 1906  2020-06-04               South East     11
## 1907  2020-06-05               South East     11
## 1908  2020-06-06               South East     10
## 1909  2020-06-07               South East     12
## 1910  2020-06-08               South East      8
## 1911  2020-06-09               South East     11
## 1912  2020-06-10               South East     11
## 1913  2020-06-11               South East      5
## 1914  2020-06-12               South East      6
## 1915  2020-06-13               South East      7
## 1916  2020-06-14               South East      7
## 1917  2020-06-15               South East      8
## 1918  2020-06-16               South East     14
## 1919  2020-06-17               South East     10
## 1920  2020-06-18               South East      4
## 1921  2020-06-19               South East      7
## 1922  2020-06-20               South East      5
## 1923  2020-06-21               South East      3
## 1924  2020-06-22               South East      2
## 1925  2020-06-23               South East      9
## 1926  2020-06-24               South East      7
## 1927  2020-06-25               South East      5
## 1928  2020-06-26               South East      8
## 1929  2020-06-27               South East      9
## 1930  2020-06-28               South East      6
## 1931  2020-06-29               South East      5
## 1932  2020-06-30               South East      5
## 1933  2020-07-01               South East      2
## 1934  2020-07-02               South East      8
## 1935  2020-07-03               South East      3
## 1936  2020-07-04               South East      6
## 1937  2020-07-05               South East      5
## 1938  2020-07-06               South East      4
## 1939  2020-07-07               South East      6
## 1940  2020-07-08               South East      3
## 1941  2020-07-09               South East      7
## 1942  2020-07-10               South East      3
## 1943  2020-07-11               South East      4
## 1944  2020-07-12               South East      5
## 1945  2020-07-13               South East      5
## 1946  2020-07-14               South East      5
## 1947  2020-07-15               South East      6
## 1948  2020-07-16               South East      3
## 1949  2020-07-17               South East      1
## 1950  2020-07-18               South East      5
## 1951  2020-07-19               South East      2
## 1952  2020-07-20               South East      6
## 1953  2020-07-21               South East      4
## 1954  2020-07-22               South East      2
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## 2463  2020-12-16               South West      9
## 2464  2020-12-17               South West     26
## 2465  2020-12-18               South West     11
## 2466  2020-12-19               South West     22
## 2467  2020-12-20               South West     19
## 2468  2020-12-21               South West     22
## 2469  2020-12-22               South West     11
## 2470  2020-12-23               South West     16
## 2471  2020-12-24               South West     18
## 2472  2020-12-25               South West     19
## 2473  2020-12-26               South West     24
## 2474  2020-12-27               South West     24
## 2475  2020-12-28               South West     21
## 2476  2020-12-29               South West     20
## 2477  2020-12-30               South West     17
## 2478  2020-12-31               South West     27
## 2479  2021-01-01               South West     29
## 2480  2021-01-02               South West     24
## 2481  2021-01-03               South West     28
## 2482  2021-01-04               South West     31
## 2483  2021-01-05               South West     31
## 2484  2021-01-06               South West     27
## 2485  2021-01-07               South West     30
## 2486  2021-01-08               South West     34
## 2487  2021-01-09               South West     26
## 2488  2021-01-10               South West     33
## 2489  2021-01-11               South West     40
## 2490  2021-01-12               South West     48
## 2491  2021-01-13               South West     40
## 2492  2021-01-14               South West     34
## 2493  2021-01-15               South West     46
## 2494  2021-01-16               South West     55
## 2495  2021-01-17               South West     35
## 2496  2021-01-18               South West     45
## 2497  2021-01-19               South West     45
## 2498  2021-01-20               South West     63
## 2499  2021-01-21               South West     59
## 2500  2021-01-22               South West     60
## 2501  2021-01-23               South West     53
## 2502  2021-01-24               South West     59
## 2503  2021-01-25               South West     59
## 2504  2021-01-26               South West     43
## 2505  2021-01-27               South West     43
## 2506  2021-01-28               South West     50
## 2507  2021-01-29               South West     41
## 2508  2021-01-30               South West     39
## 2509  2021-01-31               South West     36
## 2510  2021-02-01               South West     28
## 2511  2021-02-02               South West     36
## 2512  2021-02-03               South West     31
## 2513  2021-02-04               South West     32
## 2514  2021-02-05               South West     24
## 2515  2021-02-06               South West     38
## 2516  2021-02-07               South West     35
## 2517  2021-02-08               South West     30
## 2518  2021-02-09               South West     29
## 2519  2021-02-10               South West     17
## 2520  2021-02-11               South West     18
## 2521  2021-02-12               South West     25
## 2522  2021-02-13               South West     26
## 2523  2021-02-14               South West     16
## 2524  2021-02-15               South West     18
## 2525  2021-02-16               South West     10
## 2526  2021-02-17               South West     18
## 2527  2021-02-18               South West     19
## 2528  2021-02-19               South West     17
## 2529  2021-02-20               South West     11
## 2530  2021-02-21               South West     16
## 2531  2021-02-22               South West     10
## 2532  2021-02-23               South West      4
## 2533  2021-02-24               South West      8
## 2534  2021-02-25               South West      0

1.5 Completion date

We extract the completion date from the NHS Pathways file timestamp:


database_date <- attr(x, "timestamp")
database_date
## [1] "2021-02-25"

The completion date of the NHS Pathways data is Thursday 25 Feb 2021.

1.6 Auxiliary functions

These are functions which will be used further in the analyses.

Function to estimate the generalised R-squared as the proportion of deviance explained by a given model:


## Function to calculate R2 for Poisson model
## not adjusted for model complexity but all models have the same DF here

Rsq <- function(x) {
  1 - (x$deviance / x$null.deviance)
}

Function to extract growth rates per region as well as halving times, and the associated 95% confidence intervals:


## function to extract the coefficients, find the level of the intercept,
## reconstruct the values of r, get confidence intervals

get_r <- function(model) {
  ##  extract coefficients and conf int
  out <- data.frame(r = coef(model))  %>%
    rownames_to_column("var") %>% 
    cbind(confint(model)) %>%
    filter(!grepl("day_of_week", var)) %>% 
    filter(grepl("day", var)) %>%
    rename(lower_95 = "2.5 %",
           upper_95 = "97.5 %") %>%
    mutate(var = sub("day:", "", var))
  
  ## reconstruct values: intercept + region-coefficient
  for (i in 2:nrow(out)) {
    out[i, -1] <- out[1, -1] + out[i, -1]
  }
  
  ## find the name of the intercept, restore regions names
  out <- out %>%
    mutate(nhs_region = model$xlevels$nhs_region) %>%
    select(nhs_region, everything(), -var)
  
  ## find halving times
  halving <- log(0.5) / out[,-1] %>%
    rename(halving_t = r,
           halving_t_lower_95 = lower_95,
           halving_t_upper_95 = upper_95)
  
  ## set halving times with exclusion intervals to NA
  no_halving <- out$lower_95 < 0 & out$upper_95 > 0
  halving[no_halving, ] <- NA_real_
  
  ## return all data
  cbind(out, halving)
  
}

Functions used in the correlation analysis between NHS Pathways reports and deaths:

## Function to calculate Pearson's correlation between deaths and lagged
## reports. Note that `pearson` can be replaced with `spearman` for rank
## correlation.

getcor <- function(x, ndx) {
  return(cor(x$deaths[ndx],
             x$note_lag[ndx],
             use = "complete.obs",
             method = "pearson"))
}

## Catch if sample size throws an error
getcor2 <- possibly(getcor, otherwise = NA)

getboot <- function(x) {
  result <- boot::boot.ci(boot::boot(x, getcor2, R = 1000), 
                           type = "bca")
  return(data.frame(n = sum(!is.na(x$note_lag) & !is.na(x$deaths)),
                    r = result$t0,
                    r_low = result$bca[4],
                    r_hi = result$bca[5]))
}

Function to classify the day of the week into weekend, Monday, and the rest:


## Fn to add day of week
day_of_week <- function(df) {
  df %>% 
    dplyr::mutate(day_of_week = lubridate::wday(date, label = TRUE)) %>% 
    dplyr::mutate(day_of_week = dplyr::case_when(
      day_of_week %in% c("Sat", "Sun") ~ "weekend",
      day_of_week %in% c("Mon") ~ "monday",
      !(day_of_week %in% c("Sat", "Sun", "Mon")) ~ "rest_of_week"
    ) %>% 
      factor(levels = c("rest_of_week", "monday", "weekend")))
}

Custom color palettes, color scales, and vectors of colors:


pal <- c("#006212",
         "#ae3cab",
         "#00db90",
         "#960c00",
         "#55aaff",
         "#ff7e78",
         "#00388d")

age.pal <- viridis::viridis(3,begin = 0.1, end = 0.7)

3 Comparison with deaths time series

3.1 Outline

We want to explore the correlation between NHS Pathways reports and deaths, and assess the potential for reports to be used as an early warning system for disease resurgence.

Death data are publically available. We truncate the time series to avoid bias from reporting delay - we assume a conservative delay of three weeks.

3.2 Lagged correlation

We calculate Pearson’s correlation coefficient between deaths and NHS Pathways notifications using different lags. Confidence intervals are obtained using bootstrap. Note that results were also confirmed using Spearman’s rank correlation.

First we join the NHS Pathways and death data, and aggregate over all England:

## truncate death data for reporting delay
trunc_date <- max(dth$date_report) - delay_max

dth_trunc <- dth %>%
  rename(date = date_report) %>%
  filter(date <= trunc_date) 

## join with notification data
all_data <- x %>% 
  filter(!is.na(nhs_region)) %>%
  group_by(date, nhs_region) %>%
  summarise(count = sum(count, na.rm = T)) %>%
  ungroup %>%
  inner_join(dth_trunc,
             by = c("date","nhs_region"))

all_tot <- all_data %>%
  group_by(date) %>%
  summarise(count = sum(count, na.rm = TRUE),
            deaths = sum(deaths, na.rm = TRUE)) 

We calculate correlation with lagged NHS Pathways reports from 0 to 30 days behind deaths:


## Calculate all correlations + bootstrap CIs
lag_cor <- data.frame()
for (i in 0:30) {
  
  ## lag reports
  summary <- all_tot %>% 
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI
    getboot(.) %>%
    mutate(lag = i)

  lag_cor <- bind_rows(lag_cor, summary)
}

cor_vs_lag <- ggplot(lag_cor, aes(lag, r)) +
  theme_bw() +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi), alpha = 0.2) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_point() +
  geom_line() +
  labs(x = "Lag between NHS pathways and death data (days)",
       y = "Pearson's correlation") +
  large_txt
cor_vs_lag


l_opt <- which.max(lag_cor$r)

This analysis suggests that the best lag is 15 days. We then compare and plot the number of deaths reported against the number of NHS Pathways reports lagged by 15 days.


all_tot <- all_tot %>%
  rename(date_death = date) %>%
  mutate(note_lag = lag(count, lag_cor$lag[l_opt]),
         note_lag_c = (note_lag - mean(note_lag, na.rm = T)),
         date_note = lag(date_death,16))

lag_mod <- glm(deaths ~ note_lag, data = all_tot, family = "quasipoisson")

summary(lag_mod)
## 
## Call:
## glm(formula = deaths ~ note_lag, family = "quasipoisson", data = all_tot)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -18.672  -16.026   -5.678    6.665   33.518  
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 5.175e+00  6.908e-02  74.913   <2e-16 ***
## note_lag    1.179e-05  1.266e-06   9.314   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for quasipoisson family taken to be 227.0752)
## 
##     Null deviance: 79732  on 308  degrees of freedom
## Residual deviance: 65237  on 307  degrees of freedom
##   (15 observations deleted due to missingness)
## AIC: NA
## 
## Number of Fisher Scoring iterations: 5

exp(coefficients(lag_mod))
## (Intercept)    note_lag 
##  176.765714    1.000012
exp(confint(lag_mod))
##                  2.5 %     97.5 %
## (Intercept) 153.982927 201.892765
## note_lag      1.000009   1.000014

Rsq(lag_mod)
## [1] 0.181792

mod_fit <- as.data.frame(predict(lag_mod, type = "link", se.fit = TRUE)[1:2])

all_tot_pred <- 
  all_tot %>%
  filter(!is.na(note_lag)) %>%
  mutate(pred = mod_fit$fit,
         pred.se = mod_fit$se.fit,
         low = exp(pred - 1.96*pred.se),
         hi = exp(pred + 1.96*pred.se))


glm_fit <- all_tot_pred %>% 
    filter(!is.na(note_lag)) %>%
  ggplot(aes(x = note_lag, y = deaths)) +
  geom_point() + 
  geom_line(aes(y = exp(pred))) + 
  geom_ribbon(aes(ymin = low, ymax = hi), alpha = 0.3, col = "grey") +
  theme_bw() +
  labs(y = "Daily number of\ndeaths reported",
       x = "Daily number of NHS Pathways reports") +
  large_txt

glm_fit

4 Supplementary figures

4.1 Serial interval distribution

This is a comparison of gamma versus lognormal distribution for the serial interval used to convert r to R in our analysis. Both distributions are parameterised with mean 4.7 and standard deviation 2.9.

SI_param <- epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale, w = 0.5)

SI_distribution2 <- distcrete::distcrete("lnorm", interval = 1,
                                        meanlog = log(4.7),
                                        sdlog = log(2.9), w = 0.5)

SI_dist1 <- data.frame(x = SI_distribution$r(1e5)) 
SI_dist1 <- count(SI_dist1, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 30, 5)) +
    theme_bw()

SI_dist2 <- data.frame(x = SI_distribution2$r(1e5)) 
SI_dist2 <- count(SI_dist2, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 200, 20), limits = c(0, 200)) +
    theme_bw()


ggpubr::ggarrange(SI_dist1,
                  SI_dist2,
                  nrow = 1,
                  labels = "AUTO") 

4.2 Sensitivity analysis - 7 or 21 days moving window

We reproduce the window analysis with either a 7 or 21 days window for sensitivity purposes.

First with the 7 days window:

## set moving time window (1/2/3 weeks)
w <- 7

# create empty df
r_all_sliding_7days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_7days <- bind_rows(r_all_sliding_7days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_7days <- r_all_sliding_7days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
plot_R <- r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_7days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_7days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_7 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

Then with the 21 days window:

## set moving time window (1/2/3 weeks)
w <- 21

# create empty df
r_all_sliding_21days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_21days <- bind_rows(r_all_sliding_21days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_21days <- r_all_sliding_21days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
# plot
plot_R <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_21days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_21days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_21 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

And we combine both outputs into a single plot:


ggpubr::ggarrange(r_R_7,
                  r_R_21,
                  nrow = 2,
                  labels = "AUTO",
                  common.legend = TRUE,
                  legend = "bottom") 

4.3 Correlation between NHS Pathways reports and deaths by NHS region


lag_cor_reg <- data.frame()

for (i in 0:30) {

  summary <-
    all_data %>%
    group_by(nhs_region) %>%
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI for each region
    group_modify(~getboot(.x)) %>%
    mutate(lag = i)
  
  lag_cor_reg <- bind_rows(lag_cor_reg, summary)
}

cor_vs_lag_reg <- 
lag_cor_reg %>%
ggplot(aes(lag, r, col = nhs_region)) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi, col = NULL, fill = nhs_region), alpha = 0.2) +
  geom_point() +
  geom_line() +
  facet_wrap(~nhs_region) +
  scale_color_manual(values = pal) +
  scale_fill_manual(values = pal, guide = F) +  
  theme_bw() +
  labs(x = "Lag between NHS pathways and death data (days)", y = "Pearson's correlation", col = "NHS region") +
  theme(legend.position = "bottom") +
  guides(color = guide_legend(override.aes = list(fill = NA)))

cor_vs_lag_reg

5 Export data

We save the tables created during our analysis:


if (!dir.exists("excel_tables")) {
  dir.create("excel_tables")
}


## list all tables, and loop over export
tables_to_export <- c("r_all_sliding", "lag_cor")

for (e in tables_to_export) {
  rio::export(get(e),
              file.path("excel_tables",
                        paste0(e, ".xlsx")))
}

## also export result from regression on lagged data 
rio::export(lag_mod, file.path("excel_tables", "lag_mod.rds"))

6 System information

6.1 Outline

The following information documents the system on which the document was compiled.

6.2 System

This provides information on the operating system.

Sys.info()
##                                                                                             sysname 
##                                                                                            "Darwin" 
##                                                                                             release 
##                                                                                            "19.6.0" 
##                                                                                             version 
## "Darwin Kernel Version 19.6.0: Tue Jan 12 22:13:05 PST 2021; root:xnu-6153.141.16~1/RELEASE_X86_64" 
##                                                                                            nodename 
##                                                                           "Mac-1614420643258.local" 
##                                                                                             machine 
##                                                                                            "x86_64" 
##                                                                                               login 
##                                                                                              "root" 
##                                                                                                user 
##                                                                                            "runner" 
##                                                                                      effective_user 
##                                                                                            "runner"

6.3 R environment

This provides information on the version of R used:

R.version
##                _                           
## platform       x86_64-apple-darwin17.0     
## arch           x86_64                      
## os             darwin17.0                  
## system         x86_64, darwin17.0          
## status                                     
## major          4                           
## minor          0.4                         
## year           2021                        
## month          02                          
## day            15                          
## svn rev        80002                       
## language       R                           
## version.string R version 4.0.4 (2021-02-15)
## nickname       Lost Library Book

6.4 R packages

This provides information on the packages used:

sessionInfo()
## R version 4.0.4 (2021-02-15)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] ggnewscale_0.4.5     ggpubr_0.4.0         lubridate_1.7.10    
##  [4] chngpt_2020.10-12    cyphr_1.1.0          DT_0.17             
##  [7] kableExtra_1.3.4     janitor_2.1.0        remotes_2.2.0       
## [10] projections_0.5.2    earlyR_0.0.5         epitrix_0.2.2       
## [13] distcrete_1.0.3      incidence_1.7.3      rio_0.5.16          
## [16] reshape2_1.4.4       rvest_0.3.6          xml2_1.3.2          
## [19] linelist_0.0.40.9000 forcats_0.5.1        stringr_1.4.0       
## [22] dplyr_1.0.4          purrr_0.3.4          readr_1.4.0         
## [25] tidyr_1.1.2          tibble_3.1.0         ggplot2_3.3.3       
## [28] tidyverse_1.3.0      here_1.0.1           reportfactory_0.0.5 
## 
## loaded via a namespace (and not attached):
##  [1] minqa_1.2.4       colorspace_2.0-0  selectr_0.4-2     ggsignif_0.6.1   
##  [5] ellipsis_0.3.1    rprojroot_2.0.2   snakecase_0.11.0  fs_1.5.0         
##  [9] rstudioapi_0.13   farver_2.0.3      fansi_0.4.2       splines_4.0.4    
## [13] knitr_1.31        jsonlite_1.7.2    nloptr_1.2.2.2    broom_0.7.5      
## [17] dbplyr_2.1.0      compiler_4.0.4    httr_1.4.2        backports_1.2.1  
## [21] assertthat_0.2.1  Matrix_1.3-2      cli_2.3.1         htmltools_0.5.1.1
## [25] tools_4.0.4       gtable_0.3.0      glue_1.4.2        Rcpp_1.0.6       
## [29] carData_3.0-4     cellranger_1.1.0  vctrs_0.3.6       svglite_2.0.0    
## [33] nlme_3.1-152      matchmaker_0.1.1  crosstalk_1.1.1   xfun_0.21        
## [37] ps_1.5.0          openxlsx_4.2.3    lme4_1.1-26       lifecycle_1.0.0  
## [41] statmod_1.4.35    rstatix_0.7.0     MASS_7.3-53       scales_1.1.1     
## [45] hms_1.0.0         parallel_4.0.4    sodium_1.1        yaml_2.2.1       
## [49] curl_4.3          gridExtra_2.3     stringi_1.5.3     highr_0.8        
## [53] kyotil_2020.10-12 boot_1.3-26       zip_2.1.1         rlang_0.4.10     
## [57] pkgconfig_2.0.3   systemfonts_1.0.1 evaluate_0.14     lattice_0.20-41  
## [61] labeling_0.4.2    htmlwidgets_1.5.3 cowplot_1.1.1     tidyselect_1.1.0 
## [65] plyr_1.8.6        magrittr_2.0.1    R6_2.5.0          generics_0.1.0   
## [69] DBI_1.1.1         mgcv_1.8-33       pillar_1.5.0      haven_2.3.1      
## [73] foreign_0.8-81    withr_2.4.1       survival_3.2-7    abind_1.4-5      
## [77] modelr_0.1.8      crayon_1.4.1      car_3.0-10        utf8_1.1.4       
## [81] rmarkdown_2.7     viridis_0.5.1     grid_4.0.4        readxl_1.3.1     
## [85] data.table_1.14.0 reprex_1.0.0      digest_0.6.27     webshot_0.5.2    
## [89] munsell_0.5.0     viridisLite_0.3.0